There are about 200 people in each group at the Borghese. The doors open and if you are near the beginning of the line, you will be among the first in. The guards begin hustling people out a few minutes before the 2 hours are up. If you want to avoid the crowds, go immediately to the second floor and then make your way down to the first floor as most people are making their way upstairs. The galeries are not large, you'll have enough time to see it all without rushing.
The Vatican Museums are huge. Once you are inside, you can stay until closing. In addition to the main building to your left after you go up the escalator, there are a couple of small museums on the right and don't miss the Bramante Staircase on your right. There are gift shops throughout to galleries. Once you enter the main building, there is a one-way plan to visit which leads to the Sistine Chapel. Along the way are a few side rooms with additional collections (like the Egyptian and Etruscan). After the Sistine Chapel, there's a long walk through more much less interesting galleries to the exit. However, you can backtrack at any time before entering the Sistine Chapel, though in a couple of galleries you may feel like a salmon swimming upstream against the current. There's a cafeteria or two where you can get light food and drinks and you can relax for a while in the large courtyard too. The only place the one-way plan is strictly enforced is in the Sistine Chapel. I am pretty sure that once you exit it, there's a way to return to the galleries leading to it and eventually make your way back to the main entrance. If you don't think you'll have a lot of stamina or you don't want to spend a full day there, do some research on their website and decide which galleries you want to focus on.
The Borghese doesn't feel crowded. If there are a lot of people around a statue, go to another room and come back in 5-10 minutes. They'll be gone. OTOH many of the Vatican galleries are crowded much of the time.
